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Fujino, T.

Publications and source records attributed to Fujino, T..

16 recordsLinked to original sources

Ether-lipid deficiency remodels the testicular interstitium beyond spermatogenic arrest in Gnpat-knockout mice

Ether lipids, including plasmalogens and the germ-cell glycolipid seminolipid, require the peroxisomal enzyme GNPAT. Gnpat-knockout mice are male-infertile, but their testis has been described only qualitatively. We immunostained testis sections from 12-week-old wild-type (WT) and Gnpat-knockout (KO) mice (n = 3 per genotype) for SOX9 and {gamma}H2AX with DAPI and analysed 24 fields (22,560 nuclei) with an automated pipeline and a conservative animal-level analysis. Seminiferous tubules fell from 90% to 43% of the section, and the interstitium expanded five-fold (from 11% to 54%). Interstitial cells were 1.6-fold larger but not more densely packed, and half of them, against a quarter in WT, showed lipofuscin-like autofluorescence. Spermatid-sized nuclei fell from 38% to 10%, with the loss confined to the adluminal compartment. The architectural, interstitial and germ-cell changes held at the animal level (P [≤] 0.02). Anucleate SOX9-immunoreactive bodies, likely residual bodies, were 2.2-fold rarer, and {gamma}H2AX was not increased, which argues against a DNA-damage checkpoint arrest. Ether-lipid deficiency thus arrests germ cells, most likely through loss of seminolipid, and remodels the interstitium into an expanded compartment of enlarged, autofluorescent cells, a second target relevant to rhizomelic chondrodysplasia punctata.

physiology↗

Cohesin constrains histone modification-driven chromatin dynamics

Gene expressions are regulated by an interplay between epigenetics and spatial genome organization, the deregulation of which has been implicated in the development of cancers, including myeloid neoplasms. However, it is unclear how they coordinately contribute to normal and malignant hematopoiesis. Here, we show that simultaneous dysregulations of histone modifications and chromatin structures caused by mutations of the epigenetic modulator Asxl1 and cohesin subunit Stag2 cooperatively induce ectopic interactions between polycomb-regulated promoters and active enhancers, leading to the aberrant upregulation of hematopoietic stem cell related genes and development of myelodysplastic syndromes (MDS). De-repression of polycomb-regulated genes induces their translocation to the transcriptionally active loci, where active promoters and enhancers are assembled, in the absence of Stag2-mediated chromatin organization. Our findings revealed that cohesin counteracts histone modification-driven chromatin conformations, manifesting the coordinate roles of histone modifiers and cohesin in regulating genome architectures and gene expressions to prevent malignant transformation.

cancer biology↗

Plasmalogen-Independent Neuroprotection: Synthetic alkyl ether lipids activate signaling to mitigate neuroinflammation and enhance cognitive function

Neuroinflammation is a key driver of neurodegenerative disorders, with chronic activation of the NF-{kappa}B pathway contributing to neuronal dysfunction and disease progression. In this study, we report that KIT-8, a synthetic alkyl ether lipid, exerts potent anti-inflammatory and neuroprotective effects despite its inability to be converted into plasmalogens within cells unlike its analog KIT-13, which is known to generate plasmalogens. Remarkably, KIT-8 activates key intracellular signaling pathways, including phosphorylation of ERK and AKT, and enhances brain-derived neurotrophic factor (Bdnf) expression in Neuro2A cells, thereby mimicking the actions of both KIT-13 and natural plasmalogens. Furthermore, KIT-8 significantly improves memory function in mice, underscoring its inherent therapeutic potential. Importantly, the biological activity of KIT-8 suggests that plasmalogen synthesis is not required for its functional effects, introducing a novel concept in ether lipid biology. Supporting this notion, we identified additional alkyl ether lipid analogs, KIT-19 and KIT-20, which also demonstrated anti-inflammatory properties despite lacking the ability to generate plasmalogens. These findings indicate that the ether bond structure alone may be sufficient to confer biological activity. To explore this further, we designed and synthesized a series of structurally distinct alkyl ether lipids (KIT compounds) retaining an ether bond at the sn-2 position. In an LPS-induced inflammatory model using mouse-derived microglial MG6 cells, selected compounds KIT-8, KIT-19, and KIT-20 significantly suppressed NF-{kappa}B signaling, reduced p65 nuclear translocation, and downregulated the expression of pro-inflammatory mediators IL-1{beta} and NOS2. Given the cognitive benefits associated with plasmalogens in Alzheimers disease, our findings position alkyl ether lipids as promising standalone bioactive molecules, capable of mitigating neuroinflammation and enhancing neuronal function independently of plasmalogen synthesis.

neuroscience↗

Positional identification of a candidate gene for MALE STERILITY 2 (MS2) by linkage mapping and transcriptomic data in Cryptomeria japonica D. Don

BackgroundJapanese cedar (Cryptomeria japonica D. Don) is a major plantation species in Japan, but its abundant pollen production is a primary cause of seasonal allergic rhinitis (pollinosis). To mitigate this public health issue, the use of male-sterile cultivars has been promoted. Five types of recessive male-sterile mutations (ms1-ms5) have been identified, and the causal genes and mutations for MS1 and MS4 have been elucidated. However, the gene responsible for MS2-type male sterility remains unknown. ResultsWe aimed to identify the candidate gene responsible for MS2-type male sterility using a map-based cloning strategy. High-resolution linkage mapping localized the MS2 locus to a 1.56 cM interval on linkage group 5, corresponding to an 8.64 Mb region of the reference genome. Ninety-one genes in this region were subjected to functional annotation, gene expression analysis, and mutation screening. Among these, a single gene, SUGI_0493010, encoding a GDSL-type esterase/lipase protein (GELP), fulfilled all three criteria: it showed homology to pollen development genes in Arabidopsis thaliana, was specifically expressed in male strobili, and carried a deleterious amino acid substitution (S40F) within the predicted catalytic domain in ms2 mutant. The same mutation was also detected in a heterozygous individual (Ms2/ms2) from a separate breeding population, whose genotype was confirmed through progeny testing. Structural annotation revealed that the affected serine residue lies within the conserved GDSL motif, suggesting a functional disruption of enzymatic activity. ConclusionsOur results strongly suggest that SUGI_0493010 (GELP) is the causal gene for MS2-type male sterility in C. japonica. This finding enhances our understanding of male sterility mechanisms in conifers and provides a valuable genetic resource for breeding pollen-free trees. The study also demonstrates the effectiveness of combining genetic mapping with transcriptomic and mutational data in forest tree genomics.

genomics↗

Novel plasmalogen derivative KIT-13 restores neurological function in a mouse model of Rett syndrome by reducing neuroinflammation and restoring mitochondrial function

Neurodevelopmental disorders, including Rett Syndrome (RTT), have no functional cure and cause substantial levels of disability. Neuroinflammation is now strongly associated with both neurodevelopmental disorders and neurodegenerative diseases, providing a strong rationale for development of novel therapeutics targeting common neuroinflammatory mechanisms. RTT is caused by mutations in the methylated DNA binding factor MECP2. Mecp2-deficient (Mecp2-KO) mice, which have been extensively characterized as a mouse model of RTT, exhibit high levels of neuroinflammation, mitochondrial dysfunction, and severe neurological symptoms similar to RTT patients. KIT-13 is a novel plasmalogen derivative being developed for the treatment of neurodevelopmental disorders including RTT. This study evaluated KIT-13 in both cell-based and in vivo models for its potential to inhibit neuroinflammation and address underlying mitochondrial dysfunction, as well as effects on RTT-like neurological symptoms in the RTT mouse model. Oral administration of KIT-13 to Mecp2-KO mice significantly reduced neurological symptoms assessed by a composite score evaluating mobility, gait, hindlimb clasping, tremor, breathing, and general condition and improved the life span of the RTT model mice. In addition, KIT-13 suppressed mitochondrial DNA leakage associated with Mecp2 deficiency, and significantly suppressed neuroinflammation as measured by microglial cell morphology. These results suggest that KIT-13 may be a promising therapeutic agent for RTT and other neuroinflammation-related diseases.

neuroscience↗

De novo chemo-optogenetics through rational small-molecule design and TRAP display

Optical control of biomolecules is a powerful technique for biological research, but current tools derived from natural proteins face significant limitations. Engineering these proteins to meet researchers needs remains challenging. In this study, we present a novel approach to the de novo creation of tailored chemo-optogenetic tools. This method combines the rational design of synthetic photo-switchable molecules with in vitro selection of artificial protein binders that specifically recognize a particular conformation of these molecules. We demonstrate the utility of this approach by generating artificial proteins that bind exclusively to the cis-form of designed azobenzene derivatives. The newly created pairs enable sustained protein activation with a single light pulse and allow for precise, reversible, and repeatable switching of cellular processes using two distinct wavelengths of light in mammalian cells. This de novo technique provides tailored synthetic photoswitch-protein binder pairs, expanding the potential for optical biomolecule manipulation.

synthetic biology↗

CH-related Mutant ASXL1 Promotes Atherosclerosis in Mice via Dysregulated Innate Immunity

Certain somatic mutations confer a fitness advantage in hematopoietic stem and progenitor cells (HSPCs) over normal HSPCs, resulting in the clonal expansion of mutant blood cells1, otherwise known as clonal haematopoiesis (CH). CH is frequently observed among healthy elderly people and is closely associated with the risk of cardiovascular diseases (CVDs). The most frequently mutated genes of CH include DNMT3A, TET2, and ASXL12. Among them, even though ASXL1 mutations are clinically associated with the highest risk for developing CVDs, little is known whether and how the mutations contribute to CVDs. Here we show accelerated development of atherosclerosis and increased inflammatory monocytes in mice transplanted with the bone marrow cells (BMCs) from the mice expressing mutant ASXL1 (ASXL1-MT) selectively in hematopoietic cells. RNA sequencing analysis of the plaque-macrophages derived from BMCs expressing ASXL1-MT showed more inflammatory signatures than those from control BMCs. Mechanistically, wild-type ASXL1 inhibited innate immune signalling through direct interactions with IRAK1/TRAF6/TAK1 in the cytoplasm, while ASXL1-MT, which only interacted with TAK1, lost this regulatory function, leading to NF-{kappa}B activation. This mechanism is unique and distinct from those of CH with Tet2 or Dnmt3a mutations, where overactivation of the IL-1{beta}/NLRP3 inflammasome plays critical roles3-5. Intriguingly, IRAK1/4 inhibition decreased the number of inflammatory monocytes and attenuated the development of atherosclerosis driven by ASXL1-MT. The present work connects the mutations of an epigenetic factor, ASXL1, with inflammation and CVDs and gives an indication for the prevention of CVDs in CH.

cell biology↗

Systematic Targeting of Protein Complexes with Molecular COUPLrs

Molecular glues that engage protein complexes have transformed the study of cell biology and have had a direct impact on clinical oncology. However, the identification of new glue classes and their corresponding protein complexes has remained largely serendipitous. To overcome this challenge, we report the development of molecular COUPLrs, elaborated small molecules flanked by two cysteine-reactive warheads, as well as CONNECT, an integrated chemical proteomic platform for target deconvolution. By profiling a library of molecular COUPLrs across 13 cancer cell lines, we uncovered hundreds of proteins that can be coupled together, including in some cases in mutant selective fashions. We develop an advanced COUPLr for the oncogene EML4-ALK, which engages the fusion outside of its kinase domain, restricts protein dynamics, and disrupts EML4-ALK signaling. Collectively, molecular COUPLrs substantially expand the scope of proteins that can be chemically connected, providing an unbiased approach to identify small molecules that target protein complexes.

systems biology↗

Optineurin provides a mitophagy contact site for TBK1 activation

Tank-binding kinase 1 (TBK1) is a Ser/Thr kinase involved in many intracellular processes including innate immunity, cell cycle, and apoptosis. TBK1 is also important for phosphorylating autophagy adaptors critical in selective autophagic removal of damaged mitochondria (mitophagy). However, the mechanism by which TBK1 is activated by PINK1/Parkin-mediated mitophagy remains largely unknown. Here, we show that the autophagy adaptor OPTN provides a unique platform for TBK1 activation. The OPTN-ubiquitin and OPTN-autophagy machinery interaction axes facilitate assembly of the OPTN-TBK1 complex at a contact site between damaged mitochondria and the autophagosome formation site. This assembly point serves as a positive feedback loop for TBK1 activation by accelerating hetero-autophosphorylation of the protein. Furthermore, expression of monobodies engineered in this study against OPTN impaired assembly of OPTN at the contact sites as well as the subsequent activation of TBK1 and mitochondrial degradation. Taken together the findings reveal that a positive reciprocal relationship between OPTN and TBK1 initiates autophagosome biogenesis on damaged mitochondria.

cell biology↗

A chromosome-level genome assembly of amodel conifer plant, the Japanese cedar,Cryptomeria japonica D. Don

Japanese cedar (Cryptomeria japonica D. Don) is the most important Japanese forest tree, occupying about 44% of artificial forests in Japan, and planted in East Asia, Azores Archipelago, and some islands in the Indian Ocean. Although the huge genome of the species (ca. 11 Gb) with abundant repeat elements might have been an obstacle for genetic analysis, the species is easily propagated by cutting, flowered by plant hormones like gibberellic acid, transformed by agrobacterium, and edited by CRISPR/Cas9. These characteristics of C. japonica are preferable to make the species a model conifer for which reference genome sequences are necessary. In this study, we report the first chromosome-level assembly for C. japonica (2n = 22) using a third generation selfed progeny with an estimated homozygosity of 0.96. Young leaf tissue was used to extract high-molecular-weight DNA (>50 kb) for HiFi PacBio long read sequencing and to construct Hi-C/Omni-C library for Illumina short read sequencing. Using the 29x and 26x genome coverage of HiFi and Illumina reads, respectively, de novo assembly resulted in 2,650 contigs (9.1 Gb in total) with N50 contig size of 12.0 Mb. The Hi-C analysis mapped 97% of the nucleotides on the 11 chromosomes. The assembly was verified by comparing with a consensus linkage map of 7,785 markers. The BUSCO analysis confirmed ~91% of conserved genes. Annotations of genes, repeat elements and synteny with other Cupressaceae and Pinaceae species were performed, providing fundamental resources for genomic research of conifers.

genomics↗

The molecular clock in long-lived tropical trees is independent of growth rate

The rates of appearance of new mutations play a central role in evolution. However, mutational processes in natural environments and their relationship with growth rates are largely unknown, particular in tropical ecosystems with high biodiversity. Here, we examined the somatic mutation landscapes of two tropical trees, Shorea laevis (slow-growing) and S. leprosula (fast-growing), in central Borneo, Indonesia. Using newly-constructed genomes, we identified a greater number of somatic mutations in tropical trees than in temperate trees. In both species, we observed a linear increase in the number of somatic mutations with physical distance between branches. However, we found that the rate of somatic mutation accumulation per meter of growth was 3.7-fold higher in S. laevis than in S. leprosula. This difference in the somatic mutation rate was scaled with the slower growth rate of S. laevis compared to S. leprosula, resulting in a constant somatic mutation rate per year between the two species. We also found that somatic mutations are neutral within an individual, but those mutations transmitted to the next generation are subject to purifying selection. These findings suggest that somatic mutations accumulate with absolute time and older trees have a greater contribution towards generating genetic variation. Significance StatementThe significance of our study lies in the discovery of an absolute time-dependent accumulation of somatic mutations in long-lived tropical trees, independent of growth rate. Through a comparative analysis of somatic mutation landscapes in slow- and fast-growing species, we observed a clock-like accumulation of somatic mutations in both species, regardless of their growth rates. Although the majority of somatic mutations were restricted to a single branch, we also identified mutations present in multiple branches, likely transmitted during growth. Our findings suggest that older trees make a greater contribution towards generating genetic variation.

evolutionary biology↗

PTEN-induced kinase 1 gene single-nucleotide variants as biomarkers in adjuvant chemotherapy for colorectal cancer

BackgroundFluoropyrimidine-based adjuvant chemotherapy is globally recommended for postoperative stage III colon cancer and high-risk stage II patients. However, adjuvant chemotherapy is often associated with severe adverse events and is not highly effective in preventing recurrence. Therefore, a recurrence-prevention biomarker of adjuvant chemotherapy for colorectal cancer is necessary for providing such treatments to appropriate patients. Autophagy (including mitophagy) is activated under chemotherapy-induced stress and contributes to chemotherapy resistance. Expression of autophagy-related genes and their single-nucleotide polymorphisms are reported to be effective predictors of chemotherapy response in some cancers. Our goal was to evaluate the relationship between the single-nucleotide variants of autophagy-related genes and recurrence rates to identify the recurrence-prevention biomarkers of adjuvant chemotherapy in colorectal cancer. MethodsWe analyzed surgical or biopsy specimens from 84 patients who underwent radical surgery followed by fluoropyrimidine-based adjuvant chemotherapy at Saitama Medical University International Medical Center between January and December 2016. Using targeted enrichment sequencing, we identified single-nucleotide variants and insertions/deletions in 50 genes, including autophagy-related genes, and examined their association with colorectal cancer patient relapse rates. ResultsWe detected 560 single-nucleotide variants or insertions/deletions in the target region. The results of Fishers exact test indicated that the recurrence rate of colorectal cancer after adjuvant chemotherapy was significantly lower in patients with the single- nucleotide variants (c.1018G>A [p < 0.005] or c.1562A>C [p < 0.01]) of the mitophagy-related gene PTEN-induced kinase 1. ConclusionsThe two single-nucleotide variants of this mitophagy-related gene may be biomarkers of non-recurrence in colorectal cancer patients who received postoperative adjuvant chemotherapy.

cancer biology↗

Comprehensive analysis of the effect of mRNA sequences on translation efficiency and accuracy

Messenger ribonucleic acid (mRNA) sequences influence the translation efficiency and accuracy. To increase our knowledge of how mRNA sequences affect ribosome translation and apply the obtained information to improve the mRNA display method, we conducted a comprehensive analysis of the effect of mRNA sequences on the translation. Translation efficiency depended strongly on the three codons following the start codon. Furthermore, the codons at the ribosomal E- and P-sites strongly influence the misreading of the A-site blank codon by near-cognate transfer RNA. The purine base after the blank codon also induced a higher misread rate than that with a pyrimidine base. Based on these findings, we demonstrated construction of highly diverse monobody and macrocyclic peptide libraries that would be useful in developing functional peptides and proteins in the future.

biochemistry↗

Single-nucleotide substitution determines pollen production in Japanese cedar

Pollinosis, also known as pollen allergy or hay fever, is a global problem caused by pollen produced by various plant species1-6. The wind-pollinated Japanese cedar (Cryptomeria japonica) is the largest contributor to severe pollinosis in Japan, where increasing proportions of people have been affected in recent decades7. The MS4 (MALE STERILITY 4) locus of Japanese cedar controls pollen production, and its homozygous mutants (ms4/ms4) show abnormal pollen development after the tetrad stage and produce no mature pollen. In this study, we narrowed down the MS4 locus by fine mapping in Japanese cedar and found TKPR1 (TETRAKETIDE -PYRONE REDUCTASE) gene in this region. Transformation experiments using Arabidopsis thaliana showed that single-nucleotide substitution of CjTKPR1 determines pollen production. Broad conservation of TKPR1 beyond plant division could lead to the creation of pollen-free plant not only for Japanese cedar but also for broader plant species.

plant biology↗

Development of diagnostic PCR and LAMP markers for MALE STERILITY 1 (MS1) in Cryptomeria japonica D. Don

ObjectiveDue to the allergic nature of the pollen of Cryptomeria japonica, the most important Japanese forestry conifer, a pollen-free cultivar is preferred. Mutant trees detected in nature have been used for the production of a pollen-free cultivar. In order to reduce the time and cost needed for the production and breeding, we aimed to develop simple diagnostic molecular markers for mutant alleles of the causative gene MALE STERILITY 1 (MS1) in C. japonica. The expected function of this gene, its two dysfunctional mutations, and genetic diversity were described recently in a related study. ResultsWe have developed PCR and LAMP markers to detect mutant alleles and to present experimental options depending on available laboratory equipment. At field stations, where PCR machines are not available, LAMP markers were developed. LAMP only needs heat-blocks or a water bath to perform the isothermal amplification and assay results can be easily seen by eye. Because the causative mutations were deletions, two kinds of PCR markers, amplified length polymorphism (ALP) and allele specific PCR (ASP) markers, were developed. These assays can be carried out by capillary or agarose gel electrophoresis.

genetics↗

Identification and genetic diversity analysis of a male-sterile gene (MS1) in Japanese cedar (Cryptomeria japonica D. Don)

Identifying causative genes for a target trait in conifer reproduction is challenging for species lacking whole-genome sequences. In this study, we searched for the male-sterility gene (MS1) in Cryptomeria japonica, aiming to promote marker-assisted selection (MAS) of male-sterile C. japonica to reduce the pollinosis caused by pollen dispersal from artificial C. japonica forests in Japan. We searched for mRNA sequences expressed in male strobili and found the gene CJt020762, coding for a lipid transfer protein containing a 4-bp deletion specific to male-sterile individuals. We also found a 30-bp deletion by sequencing the entire gene of another individual with the ms1. All nine breeding materials with the allele ms1 had either a 4-bp or 30-bp deletion in gene CJt020762, both of which are expected to result in faulty gene transcription and function. Furthermore, the 30-bp deletion was detected from three of five individuals in the Ishinomaki natural forest. From our findings, CJt020762 was considered to be the causative gene of MS1. Thus, by performing MAS using two deletion mutations as a DNA marker, it will be possible to find novel breeding materials of C. japonica with the allele ms1 adapted to the unique environment of each region of the Japanese archipelago.

genetics↗